trim_minfrac: Trims by MinFrac

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

Removes metabolites with MinFrac smaller than the user specified threshold. The maximum MinFrac value is chosen from all features within a metabolite group.

Usage

trim_minfrac(object, Peak.list, search.par)

## S3 method for class 'mz'
trim_minfrac(object, Peak.list, search.par)

## S3 method for class 'monoMass'
trim_minfrac(object, Peak.list, search.par)

Arguments

object	used for method dispatch. Can be any object. See usage for details
Peak.list	data frame. Must have MinFrac column. Should contain output columns from XCMS and CAMERA, and additional columns from IHL.search, Calc.MinFrac, CAMERA.parser, Calc.corr.stat and Combine.phenodata base functions.
search.par	a single-row data frame with 11 variables containing user-defined search parameters. Must contain the columns "ppm","rt","Voidrt","Corr.stat.pos","Corr.stat.neg", "CV","Minfrac", "Endogenous", "Solvent","gen.plots", "keep.singletons".

Value

data frame Peak.list.trimmed original Peak.list containing all metabolite groups containing at least one feature that has MinFrac value greater than user specified threshold; if all MinFrac values are NA (i.e. dataset contains blanks), NULL is returned

Examples

 library(LUMA)
  # is case sensitive on Linux
  file <- system.file('extdata','Search_Parameters.txt', package = "LUMA")
  search.par <- read.table(file, sep = "\t", header = TRUE) #Ignore Warning message

  method = "mz"
  class(method) = method
  test <- trim_minfrac(Peak.list = Peaklist_Pos$From_CAMERA_with_MinFrac,
  search.par = search.par, object = method)
  nrow(Peaklist_Pos$From_CAMERA_with_MinFrac) -  nrow(test) #equals 6

  method = "monoMass"
  class(method) = method
  test <- trim_minfrac(Peak.list =
  Peaklist_Pos$Combined_Isotopes_and_Adducts, search.par = search.par, object
  = method)
  nrow(Peaklist_Pos$Combined_Isotopes_and_Adducts) - nrow(test) #equals 4

USEPA/LUMA documentation built on Aug. 29, 2020, 1:40 p.m.